rs1970734

chr11-80675280-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.532 in 151,554 control chromosomes in the GnomAD database, including 24,699 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (24699 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80573 AN: 151436 Hom.: 24684 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.532 AC: 80609 AN: 151554 Hom.: 24699 Cov.: 33 AF XY: 0.537 AC XY: 39715 AN XY: 74012

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.535

Alfa AF: 0.593 Hom.: 3877

Bravo AF: 0.515

Asia WGS AF: 0.535 AC: 1850 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.50
Dann	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1970734; hg19: chr11-80386324;